Added BioCLIP 2.5 Huge Text Embedding Files

- Updated README: fix typos, specified corrupted label removal process
- Added embeddings/txt_emb_bioclip-2.5-vith14.json embeddings/txt_emb_bioclip-2.5-vith14.npy
- both LFS tracked in `.gitattributes`
- embeddings L2-normed, 794,878 in total, dim 1024

.gitattributes

@@ -61,3 +61,4 @@ dataset/metadata/eol_metadata/taxon.tab filter=lfs diff=lfs merge=lfs -text
 dataset/metadata/eol_metadata/media_manifest.csv filter=lfs diff=lfs merge=lfs -text
 embeddings/txt_emb_species.json filter=lfs diff=lfs merge=lfs -text
 embeddings/txt_emb_bioclip-2.json filter=lfs diff=lfs merge=lfs -text
+embeddings/txt_emb_bioclip-2.5-vith14.json filter=lfs diff=lfs merge=lfs -text

embeddings/README.md

@@ -2,7 +2,7 @@
 
 Be sure to select the proper text embedding files for the model and dataset versions:
 
-## BioCLIP 2.5 Huge
+## BioCLIP 2
 
 ### Files
 
@@ -31,10 +31,11 @@ The [BioCLIP 2.5 Huge text embeddings of TreeOfLife-200M](txt_emb_bioclip-2.5-vi
 
 ## Taxonomic JSON Construction
 
-The `JSON` files were created from the [TreeOfLife-200M catalog](../catalog.parquet) (if reproducing the process, be sure to use the correct revision for the intended model) and [`VernacularName.tsv` component of the GBIF Backbone Taxonomy](https://doi.org/10.15468/39omei)  using [`make_txt_embedding_json.py`](https://github.com/Imageomics/TreeOfLife-toolbox/blob/main/processing/scripts/make_txt_embedding_json.py) through the following process:
+The `JSON` files were created from the [TreeOfLife-200M catalog](../catalog.parquet) (if reproducing the process, be sure to use the correct revision for the intended model) and [`VernacularName.tsv` component of the GBIF Backbone Taxonomy](https://doi.org/10.15468/39omei) using [`make_txt_embedding_json.py`](https://github.com/Imageomics/TreeOfLife-toolbox/blob/main/processing/scripts/make_txt_embedding_json.py) through the following process:
 * **Null Value Filtering:** Remove records where `kingdom` or `species` are `null`.
 * **Deduplication:** Rows are deduplicated based on the combination of `kingdom`, `phylum`, `class`, `order`, `family`, `genus`, and `species`. This ensures that each unique taxonomic combination appears exactly once.
     * **Common Name Handling:** Currently, the catalog metadata often contains multiple common names for a single unique taxonomic combination. During processing, **the first English common name encountered** for a given unique taxonomic combination is retained. If English is not available, the first option of any language is used. We plan future improvements to establish a definitive 1-to-1 mapping or a more comprehensive common name strategy.
+* **Corrupted Label Removal:** Records where any rank looked like an ISO-8601 timestamp `(^\d{4}-\d{2}-\d{2}T\d{2}:\d{2})` or the literal strings `true` / `false` are removed. 
 
 ### Structure
 

embeddings/txt_emb_bioclip-2.5-vith14.json

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embeddings/txt_emb_bioclip-2.5-vith14.npy

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